Showing papers in "Systematic Botany in 2007"
TL;DR: The data suggest that most traditionally recognized Solanum subgenera are not monophyletic, and provides a framework for directed sampling in further phylogenetic studies, and identifies natural groups for focused revisionary work.
Abstract: Solanum, with approximately 1,500 species, is the largest genus in the Solanaceae and includes economically important species such as the tomato, potato, and eggplant. In part due to its large size and tropical center of diversity, resolving evolutionary relationships across Solanum as a whole has been challenging. In order to identify major clades within Solanum and to gain insight into phylogenetic relationships among these clades, we sampled 102 Solanum species and seven outgroup taxa for three DNA sequence regions (chloroplast ndhF and trnT- F, and nuclear waxy) and analyzed the data using parsimony and Bayesian methods. The same major Solanum clades were identified by each data partition, and the combined analysis provided the best resolved hypothesis of relationships within the genus. Our data suggest that most traditionally recognized Solanum subgenera are not monophyletic. The Thelopodium clade is sister to the rest of Solanum, which is split into two large clades. These two large clades are further divided into at least 10 subclades, for which informal names are provided and morphological synapomorphies are proposed. The identification of these subclades provides a framework for directed sampling in further phylogenetic studies, and identifies natural groups for focused revisionary work.
239 citations
TL;DR: The reinstatement and emendation of the circumscription of Micrairoideae is proposed, which changes the acronym PACCAD to PACCMAD for this large clade of grasses and suggests the recognition of a new subfamily within thePACCAD clade.
Abstract: Phylogenetic relationships among subfamilies of the well supported PACCAD clade of Poaceae remain uncertain. Several genera such as Micraira and Eriachne were considered incertae sedis in the most recent subfamilial classification of the grasses, but these two genera formed a well-supported clade in an analysis based on chloroplast and structural data. Another genus, Isachne, traditionally classified in the Panicoideae, also formed part of this well-supported clade. Despite strong molecular support for the clade, thus far no morphological synapomorphy has been found. Nevertheless, the strongly supported monophyly of this clade allowed us to suggest the recognition of a new subfamily within the PACCAD clade. Since there was already a name available, in this paper we propose the reinstatement and emendation of the circumscription of Micrairoideae. The reinstatement of Micrairoideae changes the acronym PACCAD to PACCMAD for this large clade of grasses.
114 citations
TL;DR: Using six plastid regions, a phylogeny for 26 species of the heterosporous fern genus Marsilea is presented, and it is suggested that the presence of an inferior sporocarp tooth and the place of sporocarps maturation are homoplastic characters, and are therefore of unreliable taxonomic use at an infrageneric level.
Abstract: Using six plastid regions, we present a phylogeny for 26 species of the heterosporous fern genus Marsilea. Two well-supported groups within Marsilea are identified. Group I includes two subgroups, and is relatively species-poor. Species assignable to this group have glabrous leaves (although land leaves may have a few hairs), sporocarps lacking both a raphe and teeth, and share a preference for submerged conditions (i.e., they are intolerant of desiccation). Group II is relatively diverse, and its members have leaves that are pubescent, sporocarps that bear a raphe and from zero to two teeth, and the plants are often emergent at the edges of lakes and ponds. Within Group II, five subgroups receive robust support: three are predominantly African, one is New World, and one Old World. Phylogenetic assessment of morphological evolution suggests that the presence of an inferior sporocarp tooth and the place of sporocarp maturation are homoplastic characters, and are therefore of unreliable taxonomic use at an infrageneric level. In contrast, the presence of a raphe and superior sporocarp tooth are reliable synapomorphies for classification within Marsilea.
110 citations
TL;DR: Taxonomic revisions are made here by resurrecting two genera to contain segregate clades of Tabebuia by publishing the following new combinations: Handroanthus Mattos and Roseodendron Miranda.
Abstract: Recent molecular studies have shown Tabebuia to be polyphyletic, thus necessitating taxonomic revision. These revisions are made here by resurrecting two genera to contain segregate clades of Tabebuia. Roseodendron Miranda consists of the two species with spathaceous calices of similar texture to the corolla. Handroanthus Mattos comprises the principally yellow flowered species with an indumentum of hairs covering the leaves and calyx. The species of Handroanthus are also characterized by having extremely dense wood containing copious quantities of lapachol. Tabebuia is restricted to those species with white to red or rarely yellow flowers and having an indumentum of stalked or sessile lepidote scales. The following new combinations are published: Handroanthus arianeae (A. H. Gentry) S. Grose, H. billbergii (Bur. & K. Schum). S. Grose subsp. billbergii, H. billbergii subsp. ampla (A. H. Gentry) S. Grose, H. botelhensis (A. H. Gentry) S. Grose, H. bureavii (Sandwith) S. Grose, H. catarinensis (A. H. Gentry) S. Grose, H. chrysanthus (Jacq.) S. Grose subsp. chrysanthus, H. chrysanthus subsp. meridionalis (A. H. Gentry) S. Grose, H. chrysanthus subsp. pluvicolus (A. H. Gentry) S. Grose, H. coralibe (Standl.) S. Grose, H. cristatus (A. H. Gentry) S. Grose, H. guayacan (Seemann) S. Grose, H. incanus (A. H. Gentry) S. Grose, H. lapacho (K. Schum.) S. Grose, H. pulcherrimus (Sandwith) S. Grose, H. pumilus (A. H. Gentry) S. Grose, H. riodocensis (A. H. Gentry) S. Grose, H. selachidentatus (A. H. Gentry) S. Grose, H. serratifolius (Vahl) S. Grose, H. spongiosus (Rizzini) S. Grose, H. subtilis (Sprague & Sandwith) S. Grose and H. uleanus (Kraenzl.) S. Grose.
102 citations
TL;DR: Analyses indicate that migration into North America occurred at least twice within this primarily Old World genus, and are consistent with the notion that cultivated commercial roses have a relatively narrow genetic background.
Abstract: The genus Rosa (roses) comprises approximately 190 shrub species distributed widely throughout the temperate and subtropical habitats of the northern hemisphere. Despite numerous recent studies examining phylogenetic relationships in the genus, relationships remain obscure due to problems such as poor identification of garden specimens, hybridization in nature and in the garden, and low levels of chloroplast and nuclear genome variation. Phylogenetic analyses of non-coding chloroplast sequences from the trnL-F region and psbA-trnH intergenic spacer for 70 taxa show slightly more variation than previous analyses of the genus. Bayesian and parsimony analyses suggest that subg. Rosa can be divided into two large clades, each with low internal resolution. One comprises species from sections Carolinae, Cinnamomeae and Pimpinellifoliae p.p., whilst the other consists of all of the remaining sections of subg. Rosa (Banksianae p.p., Bracteatae, Caninae, Indicae, Laevigatae, Rosa, Synstylae and Pimpinellifoliae p.p.). A fairly complete sampling of field-collected North American taxa has been incorporated in this analysis. Analyses indicate that migration into North America occurred at least twice within this primarily Old World genus. Most North American taxa, except R. setigera and R. minutifolia, fall into a single clade that includes Asian and European taxa. Analyses also are consistent with the notion that cultivated commercial roses have a relatively narrow genetic background. Six of the seven primary taxa believed to be involved in the creation of domesticated roses are found within the same large clade that mostly includes Asian and European taxa.
92 citations
TL;DR: Corolla morphology has undergone convergent evolution and is therefore likely an inappropriate character for sectional delimitation, contrary to previous use, and Bayesian and parsimony analyses indicate four genera are evolutionarily allied to Ruellia.
Abstract: Phylogenetic relationships among species of the large genus Ruellia (Acanthaceae) have never been studied. Ruellia, with approximately 300 species, is geographically widespread and morphologically diverse. Molecular data for 196 specimens from the nuclear ribosomal ITS region and the chloroplast trnG-trnR region were used to test monophyly of the genus against closely related genera in Ruellieae, to reconstruct phylogenetic relationships among species of Ruellia on a global scale, to re-evaluate previous morphology-based classifications, and to examine the utility of morphological characters, especially corolla morphology, for future sectional delimitation. Bayesian and parsimony analyses indicate four genera are evolutionarily allied to Ruellia. Acanthopale is sister to Ruellia s. l. with strong support. Blechum, Eusiphon, and Polylychnis are nested within Ruellia s. l., and species in Eusiphon and Polylychnis are here formally transferred to Ruellia resulting in the new combinations Ruellia gea...
86 citations
TL;DR: Sequences of the chloroplast genes matK and rbcL and nuclear ribosomal ITS2 were used for phylogenetic analyses of Berberidaceae and three major clades were recognized, corresponding to the chromosome base numbers x = 6, 7, and 8/10.
Abstract: Sequences of the chloroplast genes matK and rbcL and nuclear ribosomal ITS2 were used for phylogenetic analyses of Berberidaceae. Three major clades were recognized, corresponding to the chromosome base numbers x = 6, 7, and 8/10. Bongardia was sister to the clade containing Achlys and the Podophyllum group, which consists of Diphylleia, Sinopodophyllum, Podophyllum, and Dysosma. The estimated times of divergence of six disjunct genera between Eurasia and North America ranged from 7.5 ± 2.3 Ma to 1.0 ± 0.7 Ma. The intercontinental disjunct lineages of Berberidaceae may have originated in eastern Asia and then migrated to Europe and North America. However, long-distance dispersal may explain the distribution pattern of Achlys. Desert xerophytes of Berberidaceae in southwestern Asia originated in response to the advent of dry climate at different times; Bongardia diverged from its closest relatives at 46.5 ± 3.6 Ma, whereas Leontice differentiated from Gymnospermium at 10.3 ± 3.2 Ma.
70 citations
TL;DR: The phylogeny of Tabebuia presented here corresponds to the species groups established by Gentry, while at the same time highlighting the need for taxonomic revisions.
Abstract: Tabebuia is one of the most commonly encountered genera of Bignoniaceae in the neotropics. Previous research has suggested that this genus may be paraphyletic and contain the tribe Crescentieae. Molecular sequence data of the chloroplast trnL-F and ndhF regions were used to reconstruct the phylogeny of Tabebuia, Crescentieae and related genera. A previously unrecognized clade of Neotropical, arboreal Bignoniaceae characterized by palmately compound leaves was identified and is referred to as the Tabebuia alliance. Within this group, Tabebuia is confirmed to be paraphyletic, since it includes Crescentieae, Spirotecoma, and Ekmanianthe. The position of Zeyheria, Godmania, and Cybistax with relation to Tabebuia is equivocal. Sparattosperma is sister to the rest of the Tabebuia alliance. Spirotecoma is inferred to be sister to Crescentieae. The phylogeny of Tabebuia presented here corresponds to the species groups established by Gentry, while at the same time highlighting the need for taxonomic revisions. When considered on a biogeographic scale, the phylogeny indicates a minimum of four dispersal events from the mainland to the Greater Antilles.
61 citations
TL;DR: The phylogeny of the highly disjunct Eurasian/North African Epimedium and all three species of its western North American sister genus Vancouveria is reconstructed and major splits are dated with a molecular clock approach, implying that the European mountain species are not most closely related to taxa in mountain areas towards the east but rather toTaxa in the Far East.
Abstract: Using ITS and atpB-rbcL spacer sequences of 38 (of 55) species of the highly disjunct Eurasian/North African Epimedium and all three species of its western North American sister genus Vancouveria, we reconstructed the phylogeny of these two genera and dated major splits with a molecular clock approach. Epimedium was found to be monophyletic with a stem age dated to between 9.7 and 7.4 million years ago (My). Within Epimedium, almost all sections as recognized in the most recent classification of the genus were found to be monophyletic but subg. Epimedium was found to be paraphyletic in relation to subg. Rhizophyllum. Range formation in Eurasia proceeded as follows: in a first step, the western Himalayan part of the generic distribution area (sect. Polyphyllon) was separated from the remainder, followed by a split between the Chinese distribution area (sect. Diphyllon) and the remainder, the separation of the highly disjunct range of E. pinnatum from the Caucasus plus E. perralderianum from North Africa (subg. Rhizophyllum) and the remainder, and in a last step the separation of the European E. alpinum plus the Turkish E. pubigerum from the range of the genus in Japan, Korea, northeastern China and Far Eastern Russia (sects. Epimedium and Macroceras). These results imply that the European mountain species are not most closely related to taxa in mountain areas towards the east (e.g., Caucasus, Himalayas) but rather to taxa in the Far East. Accordingly, in Epimedium the link between western Eurasia and eastern Asia apparently was not through intervening mountain regions but probably through a more northerly deciduous forest belt which does not exist any longer. The largest number of species of Epimedium is found in China (sect. Diphyllon: 44 species mainly in Hubei, Sichuan and Guizhou provinces). The age of this clade was dated to 0.52 to 0.4 My. This implies that the diversification of this group probably is the result of frequent range shifts in the Quaternary.
60 citations
TL;DR: This study confirmed the existence of three genetic races within the mesic coniferous forests of the Pacific Northwest, and inferred phylogenetic relationships within Salix sect.
Abstract: The disjunction of the mesic coniferous forests of the Pacific Northwest (PNW) has long been of interest to biogeographers, and several hypotheses have been posed to explain the disjunct distribution pattern. Analysis of intraspecific chloroplast DNA variation (1785 bp of matK and 400 bp of rpl16) in Salix melanopsis allows these hypotheses to be tested. Our study confirmed the existence of three genetic races (uncorrected sequence divergence ranged from 0.7-1.1%) within the species, which differ in distribution and ecology. The mesic race, associated with mesic coniferous forests, was the focus of this study. This race consists of two major lineages (uncorrected sequence divergence ranged up to 0.28%), one of which is associated with an apparent glacial refugium south of glaciation in the northern Rocky Mountains. The three haplotypes that comprise the first lineage are largely segregated into separate river canyons that comprise the “Greater Clearwater Refugium”. The other major lineage include...
56 citations
TL;DR: The inferred phylogeny lends support to merging these two subfamilies established by Engler based on different fruit types and shows that members of Euodia sensu lato should be placed in three different genera: Tetradium, EUodia, and Melicope.
Abstract: Plastid (trnL intron and trnL-F spacer) and nuclear (ITS-1 and ITS-2 rDNA) regions were analyzed to infer the phylogeny and evaluate the classification of Rutaceae subfamilies Rutoideae and Toddalioideae. The inferred phylogeny lends support to merging these two subfamilies established by Engler based on different fruit types. Moreover, Phellodendron, Tetradium, Toddalia, and Zanthoxylum were resolved as a clade, supporting the proposal for a 'proto-Rutaceae' group. The molecular data also showed that members of Euodia sensu lato should be placed in three different genera: Tetradium, Euodia, and Melicope. The latter two genera are more closely related to Acronychia than they are to Tetradium. Except for the discrepancy in the position of Melicope vitiflora, the cladistic results are congruent with the morphological and biochemical interpretations made by two previous authors.
TL;DR: A phylogenetic study of the genus Piptadenia with a sample of 18 of ca.
Abstract: We undertook a phylogenetic study of the genus Piptadenia with a sample of 18 of ca. 27 recognized species using DNA sequences from the plastid trnL-F and trnK/matK regions. Parsimony jackknife results support the hypothesis that Piptadenia is polyphyletic and that there are three independent lineages. The largest groups of species form a monophyletic lineage that is sister to Mimosa and corresponds closely to Piptadenia section Piptadenia sensu Barneby. Three species (P. obliqua, P. moniliformis, and P. leucoxylon) of section Pityrocarpa are sister to species of Pseudopiptadenia in a lineage with Parapiptadenia, Microlobius and Stryphnodendron. Piptadenia viridiflora is distantly related to sects. Piptadenia and Pityrocarpa. Section Piptadenia is characterized by the presence of prickles (aculei), a potential synapomorphy linking it to Mimosa, and exserted, racemose or paniculiform inflorescences of aggregated spikes. Piptadenia viridiflora has stipular spines and 1-2 axillary, spicate primary inflorescences. Species of sect. Pityrocarpa are unarmed trees (sometimes with hardened, persistent stipules) whose flowers have recurved petals and an ovary on a long gynophore. We recommend that Piptadenia viridiflora be removed to a new genus, and that Piptadenia be restricted to the other species of sect. Piptadenia. We resurrect the generic name Pityrocarpa to encompass the Pityrocarpa clade and make the following new combinations: Pityrocarpa moniliformis, Pityrocarpa obliqua ssp. brasiliensis, and Pityrocarpa leucoxylon.
TL;DR: Examination of chloroplast and nuclear data supports the hypothesis of a hybrid origin for Mespilus canescens, with Crataegus brachyacantha or its ancestor as the maternal parent, and maximum parsimony, maximum likelihood, and Bayesian analyses all corroborate the sister group relationship between CrATAegus and M espilus.
Abstract: Mespilus and Crataegus are sister genera in Rosaceae tribe Pyreae. Mespilus has been seen to comprise not only the medlar, Mespilus germanica, of western Eurasia but also the Arkansas, U.S.A. endemic, Mespilus canescens. Crataegus, on the other hand, consists of 140–200 species found throughout the northern hemisphere. Diagnoses of these two genera rely on morphological features of leaves, flowers and fruits. However, character states supposed to be diagnostic of Mespilus occur in species of Crataegus. We used two nuclear (ribosomal ITS and LEAFY intron2) and four intergenic chloroplast DNA regions (trnS-trnG, psbA-trnH, trnH-rpl2, and rpl20-rps12) to estimate the phylogeny of Mespilus and Crataegus. Maximum parsimony, maximum likelihood, and Bayesian analyses all corroborate the sister group relationship between Crataegus and Mespilus, and Crataegus brachyacantha sister to the rest of Crataegus. However, incongruence between chloroplast and nuclear data supports the hypothesis of a hybrid origin...
TL;DR: Results show that Pellaea sensu Tryon and Tryon is polyphyletic; Pellaea sections Holcochlaena and Ormopteris are distant relatives of sections Pellaea and Platyloma and have closer relationships with Doryopteris.
Abstract: Cheilanthoid ferns have a worldwide distribution and are found in rocky and seasonally dry habitats. Difficulty in deciphering natural lineages of cheilanthoids has been attributed to morphological convergence associated with adaptation to xeric environments. The goal of this study was to investigate the monophyly of the genus Pellaea by generating a DNA sequence-based cheilanthoid phylogeny. DNA sequences of the chloroplast rps4 gene and rps4-trnS intergenic spacer (IGS) were generated from 105 exemplars; chloroplast trnL-F IGS sequences were also generated from 60 of these samples. Results show that Pellaea sensu Tryon and Tryon is polyphyletic; Pellaea sections Holcochlaena and Ormopteris are distant relatives of sections Pellaea and Platyloma and have closer relationships with Doryopteris. A monophyletic circumscription of “pellaeoid” ferns is here defined to include traditional P. sect. Pellaea, P. sect. Platyloma, Astrolepis, and elements of Paragymnopteris and Paraceterach, all of which fo...
TL;DR: Combined analyses of age and biogeography data suggest that the most recent common ancestor of subg.
Abstract: The gypsophilic flora of the Chihuahuan Desert forms a large and potentially old edaphic assemblage. We examine the age and biogeography of gypsophily in Tiquilia subg. Eddya, a Chihuahuan Desert plant group entirely composed of gypsophiles (restricted to gypsum) and gypsovags (growing on and off gypsum). A strongly supported phylogeny of the subgenus was generated using sequence data from matK, ndhF, rps16, ITS, and waxy. Combined analyses of these data suggest that the most recent common ancestor of subg. Eddya was a gypsovag and that gypsophily has evolved twice. Individual DNA sequence region analyses that include a broad geographic sampling of all species in the subgenus reveal a complex evolutionary history shared among the narrowly distributed gypsophiles T. tuberculata and T. turneri and the gypsovags T. gossypina and T. mexicana, including putative hybridization. They also reveal a high level of geographically correlated intraspecific variation in the widespread gypsophile T. hispidissim...
TL;DR: Morphologically, once-pinnate leaf dissection and reticulate venation appear to be ancestral in the polystichoid ferns.
Abstract: Polystichum has often been treated as a sub-cosmopolitan genus of 180-230 species (i.e., Polystichum s.l.), but several segregate genera, such as Cyrtogonellum, Cyrtomidictyum, Cyrtomium, Phanerophlebia, and Sorolepidium, have been recognized in various treatments. Together, these genera constitute the polystichoid ferns. We used a data set of 47 species of the polystichoid ferns and three outgroups, including new rbcL sequences for six species in Asia, to address their phylogeny. Maximum-parsimony (MP) and Bayesian inference analyses were performed. The polystichoid ferns were resolved to include four major clades, the tropical American Phanerophlebia clade, the Cyrtomium s.s. clade, the Polystichum s.s. clade, and an eastern Asian clade containing Cyrtomium subser. Balansana, Cyrtogonellum, three sections of Polystichum, and Cyrtomidictyum (the BCPC clade). The Cyrtomium s.s. clade included 15 species of the genus but excluded subser. Balansana. The Polystichum s.s. clade was resolved as being monophyletic with relatively low bootstrap support, as long as Sorolepidium is included in Polystichum. The overall topology retrieved by the Bayesian analysis was similar to that of the MP tree, but generally had higher internal support. Based on the molecular phylogeny, three sections of Polystichum s.l., i.e., sect. Sphaenopolystichum, sect. Haplopolystichum, and sect. Crucifilix, may be more closely related to other members of the BCPC group. The eastern Asian BCPC group shared once-pinnate fronds, except for Polystichum sect. Sphaenopolystichum. Morphologically, once-pinnate leaf dissection and reticulate venation appear to be ancestral in the polystichoid ferns.
TL;DR: The phylogenetic relationships as inferred from molecular data resolved the intergeneric affinities but the main clades obtained are different from the groupings proposed by classifications based primarily on morphological characters.
Abstract: The tribe Detarieae s.l. (Caesalpinioideae: Leguminosae) contains a large number of genera that produce resins, but which previously had been placed in differrent generic groups. To test the monophyly of the resin-producing Detarieae and to examine phylogenetic relationships among these genera, we analyzed sequences from the chloroplast trnL intron and trnL-F spacer for more than 80 taxa and from the nuclear ribosomal Internal Transcribed Spacers (ITS) for over 50 taxa. The two chloroplast regions were highly congruent, but incongruent with the nuclear ITS data. Incongruence may be the result of hybridization, particularly in the Colophospermum and Hardwickia polyploid lineage. Resin-producing taxa are scattered among two clades, the Prioria and Detarieae s.s. clades, which together are monophyletic, but only with weak support. This group is characterized by the ability to produce bicyclic diterpenes. The phylogenetic relationships as inferred from molecular data resolved the intergeneric affinities but the main clades obtained are different from the groupings proposed by classifications based primarily on morphological characters. Based on these analyses, we propose new generic groupings that correspond to the Prioria s.s., Hardwickia, Hymenaea, Eperua s.s. and Detarium clades.
TL;DR: This study identifies the disparate lineages of the genus Aeschynomene and reveals that species with basifixed stipules (i.e., sect. Ochopodium) perhaps should be ranked as a distinct genus and validate the infrageneric classification of Machaerium.
Abstract: Phylogenetic relationships among the genera Dalbergia, Machaerium, and Aeschynomene were investigated with sequences from both the chloroplast DNA trnL intron and the nuclear ribosomal DNA ITS/5.8S region. A parsimony and Bayesian analysis of individual and combined data resolved a monophyletic Dalbergia that is sister to a clade comprising Aeschynomene sect. Ochopodium and Machaerium. Aeschynomene sect. Aeschynomene is paraphyletic with respect to genera such as Bryaspsis and Soemmeringia, which collectively are sister to the Dalbergia-Machaerium-Ochopodium clade. This study identifies the disparate lineages of the genus Aeschynomene and reveals that species with basifixed stipules (i.e., sect. Ochopodium) perhaps should be ranked as a distinct genus. Species of Ochopodium have the general lomented fruit morphology in contrast to the unique indehiscent samara fruits of Machaerium. The findings of this analysis also have some bearing at the infrageneric level. Limited sampling of Dalbergia sects. Triptolemea and Ecastaphyllum resolves them as monophyletic. In contrast, the traditional infrageneric classification of Machaerium does not show much agreement with molecular groups. Additional sampling of Aeschynomene and Machaerium species, other DNA sequences, and morphological data are needed to resolve the exact relationship of sect. Ochopodium to Machaerium, as well as validate the infrageneric classification of Machaerium.
TL;DR: New and existing data in phylogenetic analyses based on trnL-F, ITS, and pistillata intron 1 data are used along with SEM studies of Synthlipsis elata and S. greggii to provide the bases for recircumscription of taxa assigned to the Halimolobeae.
Abstract: In 2002, a monophyletic group previously unrecognized within Brassicaceae was identified through phylogenetic analysis of morphological characters in combination with data from three DNA sequences (Bailey et al.: Syst. Bot. 27: 318-332). As understood at that time, the halimolobine alliance (herein tribe Halimolobeae) comprised ca. 44 species from Halimolobos, Mancoa, Pennellia, and Sphaerocardamum. Within this group, a number of nomenclatural problems have remained unaddressed, including the polyphyly of both Halimolobos and Mancoa. With a developing understanding of Brassicaceae phylogeny, the Halimolobeae is robust in the context of higher level analyses and therefore in need of formal nomenclatural revision. The present study uses new and existing data in phylogenetic analyses based on trnL-F, ITS, and pistillata intron 1 data along with SEM studies of Synthlipsis elata and S. greggii to provide the bases for recircumscription of taxa assigned to the Halimolobeae. As recognized herein, the tribe includes five genera (Exhalimolobos, Halimolobos (including Synthlipsis elata), Mancoa, Pennellia, and Sphaerocardamum) and 39 species with two centers of distribution, one in north-central Mexico and the other in the Andes. A synopsis and keys to all taxa of the tribe are presented. Fifteen new combinations are proposed (E. arabioides, E. berlandieri, E. burkartii, E. hispidulus, E. palmeri, E. parryi, E. pazense, E. polyspermus, E. weddellii, H. elatus, H. henricksonii, H. pubens, H. stylosus, P. lechleri, and P. parvifolia).
TL;DR: Molecular phylogenetic analyses using the chloroplast marker ndhF and a single copy nuclear marker, knotted1, show that the panicoid grasses bearing sterile branches in their inflorescences form a monophyletic group, suggesting that inflorescence form is easily changed over evolutionary time.
Abstract: Molecular phylogenetic analyses using the chloroplast marker ndhF and a single copy nuclear marker, knotted1, show that the panicoid grasses bearing sterile branches (bristles) in their inflorescences form a monophyletic group. The genus Cenchrus is monophyletic, and monophyly of Pennisetum cannot be ruled out. Setaria is not monophyletic, either as a whole, excluding the palm-leaved species from section Ptychophyllum ,o r excluding various uncertainly placed species such as S. grisebachii. There is also no evidence that Setaria and Paspalidium form a monophyletic group. The Australian genera Zygochloa, Spinifex, and Pseudoraphis are placed in the 'bristle clade', confirming that inflorescences of these grasses are homologous with the inflorescences composed of spikelets and sterile branchlets (bristles). Comparison of the nuclear and chloroplast gene trees identifies several taxa as tetra- or higher polyploids; these are confirmed by southern hybridization. In particular, the Australian species of Paspalidium are allopolyploid, a novel and unexpected result. Zuloagaea bulbosa, a species that lacks the synapomorphic bristles in its inflorescence, is confirmed as a morphologically anomalous member of the clade, and is clearly allopolyploid. This study demonstrates the utility of knotted1 as a phylogenetic marker; we show that it is single copy in diploid taxa and that it exhibits adequate variation to distinguish closely related species. Interestingly, inflorescence morphology correlates only partially with relationships suggested by either nuclear or chloroplast trees, suggesting that inflorescence form is easily changed over evolutionary time.
TL;DR: In the combined analysis, monophyly of Lymania is moderately supported, and the genus is closely related to species of Aechmea subg.
Abstract: A cladistic analysis of Lymania was conducted using morphology and sequences from three chloroplast DNA regions: the matK coding region and the psbA-trnH and trnL-trnF intergenic spacers. The monophyly of the genus and the phylogenetic relationships among related genera were examined. Of the nine Lymania species, eight are endemic to southern Bahia, Brazil. Lymania is the first genus in Bromeliaceae subfamily Bromelioideae to be subjected to a combined morphological and molecular analysis. The genera of Bromelioideae have been particularly difficult to classify and there has been disagreement about their interrelationships and monophyly. Morphological data show better resolution than molecular data alone. The partition homogeneity test supported a combined analysis of the two data sets, yielding a single most parsimonious tree. In the combined analysis, monophyly of Lymania is moderately supported, and the genus is closely related to species of Aechmea subg. Lamprococcus and subg. subg. Ortigiesia. The morphological distinctiveness coupled with low molecular divergence indicates relatively recent and rapid speciation within Lymania. The combined analysis of morphological and molecular data as done in this study provides a framework for future research on other Bromelioideae genera that could foster better taxonomic rearrangements.
TL;DR: A classification tree showed that it is indeed feasible to identify species in the polyploid complex of Rosa sect.
Abstract: This study investigates species boundaries in the polyploid complex of Rosa sect. Cinnamomeae east of the Rocky Mountains. This complex is characterized by extensive intra-specific polymorphism that is the consequence, in part, of hybridization and polyploidy. An objective multivariate approach is employed to delimit species in the complex, which involved cluster and ordination analyses of 25 quantitative morphological characters and of amplified fragment length polymorphisms (AFLPs). Because polyploid individuals blurred species boundaries in the complex, they were discriminated a priori using stomata guard cell lengths in order to investigate species boundaries at each ploidy level separately. Four distinct species were found at the diploid level: R. blanda – R. woodsii, R. foliolosa, R. nitida and R. palustris. According to the morphological and molecular data, R. blanda and R. woodsii are indistinguishable and should be considered as a single species. Three species were identified at the poly...
TL;DR: Incongruence among nuclear and chloroplast datasets, together with the phylogenetic positions, sympatric distributions, and morphological intermediacy of discordant taxa, suggest possible reticulate evolution among members of Rhus.
Abstract: A phylogenetic analysis of Rhus (Anacardiaceae) was conducted using nuclear and chloroplast sequences. The nuclear (Nia-i3) and chloroplast (trnC-trnD) sequence data generated in this study were compared with previously published phylogenies of Rhus based on nuclear ribosomal ITS data and chloroplast trnL-F and ndhF sequences. The Nia-i3 data provided more parsimony-informative characters than ITS; the trnC-trnD data provided the most parsimony-informative characters among three chloroplast markers. All data sets support the monophyly of Rhus. Within Rhus, nuclear data support the monophyly of subgen. Lobadium and the monophyly of subgen. Rhus. Chloroplast data suggest a paraphyletic subgenus Lobadium with R. microphylla and R. rubifolia of subgen. Lobadium placed within subgen. Rhus. Rhus coriaria and R. michauxii of subgen. Rhus also have discordant positions in cpDNA and nuclear trees. Each species with discordant positions (R. coriaria, R. microphylla, R. michauxii and R. rubifolia) has a single allele or different alleles of the same species forming a monophyletic group in the nuclear ITS and Nia-i3 data. Incongruence among nuclear and chloroplast datasets, together with the phylogenetic positions, sympatric distributions, and morphological intermediacy of discordant taxa, suggest possible reticulate evolution among members of Rhus.
TL;DR: The first phylogenetic study of the subgenus Cuscuta using nuclear ITS rDNA and chloroplast trnL intron sequences is presented and several individuals of particular taxonomic difficulty or wide geographical distribution were sampled.
Abstract: Within the parasitic genus Cuscuta, three subgenera have been recognized based on characters of the styles and stigmas. Cuscuta subgenus Cuscuta, with free styles and conical to elongated stigmas, is the most diversified in the Old World with about 25 species. We present the first phylogenetic study of the subgenus using nuclear ITS rDNA and chloroplast trnL intron sequences. Sequences of almost all species of the subgenus were obtained and several individuals of particular taxonomic difficulty or wide geographical distribution were sampled. Both maximum parsimony and Bayesian analyses were performed to evaluate the monophyly of the sections previously accepted in Yuncker's monograph and to investigate phylogenetic relationships between the species. The monophyly of the subgenus could not be tested with our sampling but using three species of subgenus Monogyna as outgroup, the South African section Pachystigma was sister to the remaining species of subgenus Cuscuta. Section Epistigma plus C. capitata are resolved as monophyletic in all analyses. The distinctive C. babylonica was sister to that clade on the ITS trees but it was not resolved on the trnL trees. Two monophyletic groups within section Cuscuta, first identified here, included the species of tropical African distribution in one case and C. europaea, C. approximata, and C. balansae in the other. Factors influencing the taxonomic difficulty of many species in the subgenus include lack of morphological characters, parallelism and gene flow between closely and not so closely related species. Evidence of reticulation events or within species recombination were obtained by both polyphyletic intra-individual ITS sequences and conflicting topologies of the nuclear and plastid trees.
TL;DR: Monophyly of Piptochaetium was confirmed by morphological and total evidence (morphological and DNA data) analyses, and relationships among species of this genus and allied genera of Stipeae were analyzed.
Abstract: The tribe Stipeae occurs in temperate and warm temperate grasslands of Eurasia, Australia, and America. Although generic circumscription within the tribe has recently undergone significant changes, the American genus Piptochaetium has been clearly defined by morphological and anatomical characters. It includes 36 species and 2 varieties, most of them widely distributed in temperate grasslands of South America. Phylogenetic analyses were conducted in Piptochaetium and allied genera of the Stipeae, in order to test the monophyly of the genus, re-examine infrageneric taxa, and analyze relationships among species of this genus and allied genera of Stipeae. Two chloroplast molecular markers, trnL-F and rpl16, as well as morphology were used. Topology between morphological and molecular data mainly differs in the relationships of Piptochaetium with Anatherostipa and Piptatherum. Molecular and combined analyses yielded two major clades in the tribe: the x = 11 Clade with Piptochaetium, Aciachne, Anath...
TL;DR: The present analyses indicate that nomenclatural changes will be needed to reflect more accurately relationships in the Gibbosaccus-Chiritopsis complex and reconsider the morphological evolution and adaptation between and within the two genera.
Abstract: Sequences from the internal transcribed spacer region of nuclear DNA (ITS) and the trnL-F regions of chloroplast DNA for fifteen species of Chirita and seven species of Chiritopsis were used to assess phylogenetic relationships between Chiritopsis and Chirita section Gibbosaccus Parsimony and Bayesian inference (BI) analyses were conducted using separate nuclear and chloroplast data sets, as well as a combined data set Phylogenetic trees resulting from separate analyses proved highly congruent and the combined analysis of the two data sets produced a well-supported topology of the species and sections examined Section Gibbosaccus proved paraphyletic and Chiritopsis polyphyletic in all analyses Our results provide evidence that the species of Chiritopsis are embedded in section Gibbosaccus and were derived at least twice from within section Gibbosaccus Finally, we reconsider the morphological evolution and adaptation between and within the two genera The present analyses indicate that nomenclatural changes will be needed to reflect more accurately relationships in the Gibbosaccus-Chiritopsis complex Only about 10% of the species in Chirita have been sampled and further data are required before any taxonomic changes can be suggested
TL;DR: The results of this study show high resolution at the species level, especially within the largest genus, Chamaedorea, indicating that plastid DNA is useful for the inference of relationships at low taxonomic levels in some groups of palms.
Abstract: This study presents the first phylogenetic analysis of tribe Chamaedoreeae (Arecaceae), using parsimony and Bayesian analyses of plastid DNA sequences (matK, rps16 intron, 3′ region of ndhF, and trnD-trnT). The tribe includes more than 115 species, and has a disjunct distribution with four genera in Central and South America and one genus in the Mascarene Islands. While the placement of Chamaedoreeae within Arecaceae has been controversial, the monophyly of this tribe is well supported by plastid DNA sequence data. All genera in Chamaedoreeae are resolved as monophyletic with high support, but relationships among genera are not fully resolved. The placement of Hyophorbe and the monotypic Wendlandiella as sisters to the remaining genera indicates that solitary flowers and dioecy arose at least twice within this tribe, once in Wendlandiella and once in Chamaedorea. Although a low substitution rate of palm plastid DNA has been widely noted, the results of this study show high resolution at the speci...
TL;DR: A Hybrid Detection Criterion (HDC) is presented along with a statistical procedure that allows for the identification of hybrid taxa and it is shown how the procedure can be used as a tool to identify putative hybrids.
Abstract: The occurrence of reticulations in the evolutionary history of species poses serious challenges for all modern practitioners of phylogenetic analysis. Such events, including hybridization, introgression, and lateral gene transfer, lead to evolutionary histories that cannot be adequately represented in the form of phylogenetic trees. Although numerous methods that allow for the reconstruction of phylogenetic networks have been proposed in recent years, the detection of reticulations still remains problematic. In this paper we present a Hybrid Detection Criterion (HDC) along with a statistical procedure that allows for the identification of hybrid taxa. The test assesses whether a putative hybrid is consistently intermediate between its postulated parents, with respect to the other taxa. The performance of the statistical method is evaluated using known hybrids of the genus Aphelandra (Acanthaceae) using two network methods: reticulograms and split decomposition graphs. Our results indicate that the HDC test is reliable when used jointly with split decomposition. On the other hand, the test lacks power and provides misleading results when using reticulograms. We then show how the procedure can be used as a tool to identify putative hybrids.
TL;DR: Within annuals, Anthoxanthum gracile is clearly differentiated morphologically, yet no compelling morphological differentiation can be found between AnthoxAnthum aristatum and Anthxanthum ovatum, and the definition of subspecies in the annual taxa is not supported by the results.
Abstract: In the present study, several multivariate analyses were carried out to assess the taxonomic relationships among European species of the genus Anthoxanthum. A total of 1787 Anthoxanthum specimens representing all European taxa were analyzed. Thirty macro-morphological (13 quantitative and 17 qualitative) and 29 micro-morphological (7 quantitative and 22 qualitative) characters were considered. First, resemblances between specimens were established independently for macro- and micro-morphological characters using Gower's similarity coefficient, and were represented by means of principal coordinates and cluster analyses. Subsequently, different multivariate analyses were applied to quantitative and qualitative macromorphological data to determine the most discriminant characters and the accuracy of the present taxonomic structure of the genus. Finally, dissimilarities among groups of individuals -species and populations- were estimated using the information radius measure and then represented in different dendrograms. Within annuals, Anthoxanthum gracile is clearly differentiated morphologically, yet no compelling morphological differentiation can be found between Anthoxanthum aristatum and Anthoxanthum ovatum. Moreover, the definition of subspecies in the annual taxa is not supported by our results. Then, within perennials, although the morphological relationships among Anthoxanthum amarum, Anthoxanthum odoratum and Anthoxanthum alpinum have also been resolved, further research is needed to assess the taxonomic position of the Macaronesian endemic Anthoxanthum maderense.
TL;DR: A chloroplast DNA phylogeny is generated using intergenic spacers from a sampling of cultivars of Bactris gasipaes as well as putative wild relatives and other members of the genus Bactries to indicate a close affinity between three taxa: B. gasipAes, B. chichagui, and B. riparia.
Abstract: Peach palm (Bactris gasipaes Kunth.) is the only Neotropical palm domesticated since pre-Columbian times. It plays an important role not only at the local level due to its very nutritious fruits, but also in the international market for its gourmet palm heart. Phylogenetic relationships of the peach palm with wild Bactris taxa are still in doubt, and have never been addressed using molecular sequence data. We generated a chloroplast DNA phylogeny using intergenic spacers from a sampling of cultivars of Bactris gasipaes as well as putative wild relatives and other members of the genus Bactris. We estimated phylogenetic relationships using maximum parsimony (MP), maximum likelihood (ML), and Bayesian analysis. Our results indicated a close affinity between three taxa: Bactris gasipaes var. gasipaes, B. gasipaes var. chichagui, and B. riparia. There was no clear differentiation between these three taxa at the level of chloroplast sequences, and they shared a unique inversion that we characterized in this paper. Bactris setulosa, a species potentially related to the Bactris gasipaes complex, appeared highly divergent, and seemed to be a composite taxon with affinities outside the complex. We also investigated nuclear microsatellite polymorphisms at 8 loci within Bactris gasipaes, B. riparia, and B. setulosa, finding a pattern of relationships in agreement with the cpDNA data. The results presented here are important for future studies on domestication and crop improvement of Bactris gasipaes.